Intratumor heterogeneity may lead to sampling bias and may present major challenges to personalized medicine and biomarker development. Despite many studies investigating genetic heterogeneity, epigenetic intratumor heterogeneity of promoter hypermethylation has only rarely been examined in breast cancer. To examine clonal intratumor heterogeneity of promotor hypermethylation, we performed methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) for 24 established tumor-suppressor genes on multiple spatially separated samples obtained from 21 primary breast carcinomas. Multiregion analysis was performed, representing at least two and a maximum of five tumor blocks per patient and four areas per tumor block. Methylation results were heterogeneous at one or more genetic loci between different tumor regions in 95% of breast carcinomas. The most heterogeneous loci in decreasing frequency were RASSF1A (62%), CDKN2B (43%), APC (38%), GSTP1 (33%), CDH13 (24%), DAPK1 (19%), and CDKN1B (5%). Heterogeneity lead to a methylation status change in at least one locus in 65% of the tumors. For most genes, the relative contribution of between-patients and between-block variability to the total variation in methylation results was similar. Regardless of the gene, contribution of within-block variability was of little importance. In conclusion, although most variation in methylation status is present between individual breast cancers, clonal epigenetic heterogeneity is seen within most primary breast carcinomas, indicating that methylation results from a single random sample may not be representative of the whole tumor.